Abstract

We present a comprehensive and efficient gene set analysis tool, called GeneTrail that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the p-value computation of GSEA methods considerably.

News

New analyses/updates/organisms available

We now provide the following additional analyses:

Wilcoxon-Mann-Whitney test for the distribution of SNPs (from NCBI dbSNP) and Homologues (from NCBI Homologene) in test versus reference set

ORA/GSEA for Pfam and Cath protein domains

ORA/GSEA for miRNA target genes (from Sanger miRBase)

ORA/GSEA for OMIM categories

Furthermore, we added support for standard file formats for gene sets (.gmt,.gmx) which can be used as input for our self-defined category analysis.

GeneTrailExpress paper published

The official GeneTrailExpress paper was published in the BMC Bioinformatics journal: